rs1558902

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001080432(FTO):c.46-40478T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151844 control chromosomes in the gnomAD Genomes database, including 8801 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.31 ( 8801 hom., cov: 31)

Consequence

FTO
NM_001080432 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.355

Links

FTO (HGNC:24678):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FTO	NM_001080432.3 linkuse as main transcript	c.46-40478T>A		intron_variant		ENST00000471389.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FTO	ENST00000471389.6 linkuse as main transcript	c.46-40478T>A		intron_variant		1	NM_001080432.3	P1	Q9C0B1-1

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46860

AN:

151844

Hom.:

8801

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.489

Gnomad AMR

AF:

0.289

Gnomad ASJ

AF:

0.511

Gnomad EAS

AF:

0.154

Gnomad SAS

AF:

0.332

Gnomad FIN

AF:

0.424

Gnomad MID

AF:

0.389

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.337

Alfa

AF:

0.390

Hom.:

6856

Bravo

AF:

0.285

Asia WGS

AF:

0.270

AC:

941

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

Cadd

Benign

1.6

Dann

Benign

0.65

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over